A small Christian college in Massachusetts has come under fire for petitioning President Obama to be exempted from an order that prohibits federal contractors from discriminating based on a person’s sexual orientation.

Gordon College, which has about 2,100 students, was the lone institution of higher learning to join a slew of religious organizations and charities in signing a letter to Obama that asked for an exemption.

“A religious exemption in this executive order would not guarantee that religious organizations would receive contracts,” reads the letter, which was sent last week. “Instead, a religious exemption would simply maintain that religious organizations will not be automatically disqualified or disadvantaged in obtaining contracts because of their religious beliefs.”

That isn’t exactly how some alumni and affiliates of the college interpreted the request. Some of them started a Moveon.org petition calling on Gordon to pull back its exemption request.

“We the alumni, students, family and friends of Gordon College are requesting that President D. Michael Lindsay rescind his request to be allowed to discriminate against LGBT people in the hiring process,” said the petition, which has now been signed by nearly 3,000 people.

“While we recognize the variety of beliefs based in Holy Scripture, we do not believe that there is a Biblical requirement to refuse employment to people of LGBT sexual orientation,” it continued.

Now the school is making the case that it never intended to discriminate based on sexual orientation in hiring or admissions.

In an open letter to the Gordon community, Lindsay expressed his “sincere regret” that his signature on the letter had been “misconstrued” and thrust the school into the public eye in an unflattering way.

“Be assured that nothing has changed in our position regarding admission or employment,” Lindsay wrote on Monday. “We have never barred categories of individuals from our campus and have no intention to do so now.

“We have always sought to be a place of grace and truth, and that remains the case.”

Other groups that signed on to the letter included some of the largest Christian charitable organizations, including Catholic Charities USA and World Relief, as well as some Obama allies, including his 2012 National Faith Vote Director Michael Wear.

But the tiny Massachusetts college seemed to take the brunt of the fallout.

On Wednesday, the mayor of Salem, Mass. dropped the city’s contract with Gordon College to manage its Old Town Hall facility, citing a non-discrimination ordinance.

“While I respect your right to embed religious values on a private college campus, religious freedom does not afford you the right to impose those beliefs upon others and cannot be extended into a publicly owned facility or any management contract for a public owned facility, like Old Town Hall,” wrote Mayor Kim Driscoll.

Obama has not signed the non-discrimination executive order yet, but the religious exemption proposed in last week’s letter would mirror a similar provision in a Senate bill that would bar all employers from discrimination based on sexual orientation.

The about-face is part of the fallout from the recent Supreme Court decision in favor of a privately-owned craft store Hobby Lobby and another private company whose owners challenged a portion of the federal health care law that requires companies to cover birth control as part of their health plans.

The Supreme Court ruled that privately-owned businesses do not have to provide contraception if it contradicts its owners’ sincerely held religious beliefs.

LGBT groups fear that the Hobby Lobby ruling would open the door to private companies challenging the non-discrimination law on the basis of their religious faith.